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Commit 5815aa60 authored by Andrey Aristov's avatar Andrey Aristov
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manual correction

parent a51d6cee
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src/napari_segment/_widget.py
+ 100
− 24
View file @ 5815aa60
......@@ -27,7 +27,7 @@ from matplotlib.backends.backend_qt5agg import (
NavigationToolbar2QT as NavigationToolbar,
)
from matplotlib.figure import Figure
from napari.layers import Image
from napari.layers import Image, Labels
from napari.utils.notifications import show_error, show_info
from scipy.ndimage import (
binary_erosion,
......@@ -75,11 +75,24 @@ class SegmentStack(q.QWidget):
self.input = w.ComboBox(
label="BF data",
annotation=Image,
choices=[
layer.name
for layer in self.viewer.layers
if isinstance(layer, Image)
choices=self.update_images(),
)
self.stat_layer_selector = w.ComboBox(
label="Labels to quantify",
annotation=Labels,
choices=self.update_labels(),
)
self.btn_make_manual_labels = w.PushButton(text="Clone for manual correction")
self.btn_make_manual_labels.clicked.connect(self.make_manual_layer)
self.stat_layer_selector_container = w.Container(
widgets=[
self.stat_layer_selector,
self.btn_make_manual_labels
],
layout="horizontal"
)
self.binning_widget = w.RadioButtons(
......@@ -122,8 +135,24 @@ class SegmentStack(q.QWidget):
self.btn_save_params = q.QPushButton("Save params!")
self.btn_save_csv = q.QPushButton("Save csv!")
self.check_auto_plot = w.CheckBox(label="Update Plots")
self.check_auto_plot.changed.connect(self.plot_stats)
self.check_auto_plot = w.CheckBox(label="Auto Update")
self.check_auto_plot.changed.connect(
partial(
self.plot_stats, force=True
)
)
self.btn_update_stats = w.PushButton(text="Update plots")
self.btn_update_stats.clicked.connect(self.plot_stats)
self.update_plot_container = w.Container(
widgets=[
self.btn_update_stats,
self.check_auto_plot
],
layout='horizontal'
)
self.pixel_size = 1
self.pixel_unit = "px"
......@@ -178,7 +207,8 @@ class SegmentStack(q.QWidget):
self.setLayout(q.QVBoxLayout())
self.layout().addWidget(self.container.native)
self.layout().addWidget(self.btn_save_params)
self.layout().addWidget(self.check_auto_plot.native)
self.layout().addWidget(self.update_plot_container.native)
self.layout().addWidget(self.stat_layer_selector_container.native)
self.layout().addWidget(self.pixel_block.native)
self.layout().addWidget(self.canvas)
self.layout().addWidget(NavigationToolbar(self.canvas, self))
......@@ -192,7 +222,7 @@ class SegmentStack(q.QWidget):
self.input.changed.connect(self.preprocess)
self.canvas.mpl_connect("button_press_event", self.onfigclick)
self.canvas.mpl_connect("pick_event", self.on_pick)
# self.canvas.mpl_connect("pick_event", self.on_pick)
logger.debug("Initialization finished.")
......@@ -200,6 +230,40 @@ class SegmentStack(q.QWidget):
self.restore_params()
self.preprocess()
def update_labels(self):
return [
layer.name
for layer in self.viewer.layers
if isinstance(layer, Labels)
]
def update_images(self):
return [
layer.name
for layer in self.viewer.layers
if isinstance(layer, Image)
]
def make_manual_layer(self):
try:
clone = self.selected_labels.compute()
layer = self.viewer.add_labels(
data=clone,
name=(manual_layer_name := "Manual Labels"),
scale=self.scale,
metadata={
"binning": self.binning,
"source": self.viewer.layers["selected labels"]
}
)
self.stat_layer_selector.choices = self.update_labels()[::-1]
self.plot_stats(force=True)
except Exception as e:
show_error(err := f"Unable to create manual layer: {e}")
logger.error(err)
def move_step(self, slice):
cur_ = self.viewer.dims.current_step
new_ = list(cur_)
......@@ -330,7 +394,7 @@ class SegmentStack(q.QWidget):
if not (name := "Preprocessing") in self.viewer.layers:
logger.debug("No Preprocessing layer found, adding one")
self.viewer.add_image(
self.layer_with_preprocessing = self.viewer.add_image(
data=self.smooth_gradient,
**{"name": name, "scale": self.scale},
)
......@@ -339,8 +403,8 @@ class SegmentStack(q.QWidget):
f"Updating Preprocessing layer with \
{self.smooth_gradient}"
)
self.viewer.layers[name].data = self.smooth_gradient
self.viewer.layers[name].scale = self.scale
self.layer_with_preprocessing.data = self.smooth_gradient
self.layer_with_preprocessing.scale = self.scale
logger.debug(
f"Preprocessing finished, \
......@@ -364,7 +428,7 @@ class SegmentStack(q.QWidget):
)
if not (name := "Detections") in self.viewer.layers:
logger.debug("No Detections layer found, adding one")
self.viewer.add_labels(
self.layer_with_detections = self.viewer.add_labels(
data=self.labels,
opacity=0.3,
**{"name": name, "scale": self.scale},
......@@ -372,10 +436,10 @@ class SegmentStack(q.QWidget):
else:
logger.debug(f"Updating Detections layer with {self.labels}")
self.viewer.layers[name].data = self.labels
self.viewer.layers[name].scale = self.scale
self.layer_with_detections.data = self.labels
self.layer_with_detections.scale = self.scale
self.viewer.layers[name].contour = 8 // self.binning
self.layer_with_detections.contour = 8 // self.binning
logger.debug(
f"Thresholding succesful. \
......@@ -409,7 +473,7 @@ class SegmentStack(q.QWidget):
if not (name := "selected labels") in self.viewer.layers:
logger.debug("No selected labels layer found, adding one")
self.viewer.add_labels(
self.layer_with_selected_labels = self.viewer.add_labels(
data=selected_labels,
opacity=0.5,
**{"name": name, "scale": self.scale},
......@@ -417,30 +481,42 @@ class SegmentStack(q.QWidget):
else:
logger.debug(f"Updating labels layer with {selected_labels}")
self.viewer.layers[name].scale = self.scale
self.viewer.layers[name].data = selected_labels
# self.save_params()
self.layer_with_selected_labels.scale = self.scale
self.layer_with_selected_labels.data = selected_labels
except TypeError as e:
show_error(f"Relax filter! {e}")
self.stat_layer_selector.choices = self.update_labels()[::-1]
# self.stat_layer_selector.current_choice = "selected labels"
try:
self.plot_stats()
except Exception as e:
show_error(f"Plot failed: {e}")
def plot_stats(self, ignore_check_auto_plot=False):
def plot_stats(self, force=False):
if not self.stat_layer_selector.current_choice:
return
if not self.check_auto_plot.value:
if not ignore_check_auto_plot:
if not force:
return
self.pixel_size = float(self.pixel_size_widget.value)
self.pixel_unit = str(self.pixel_unit_widget.value)
self.ax[1].set_title(f"{self.diams_title}, {self.pixel_unit}")
data = self.viewer.layers[
self.stat_layer_selector.current_choice
].data
if isinstance(data, dask.array.Array):
data = data.compute()
props = [
regionprops(label_image=img)
for img in self.selected_labels.compute()
for img in data
]
num_regions_per_frame = [len(p) for p in props]
area_ = [
......@@ -481,7 +557,7 @@ class SegmentStack(q.QWidget):
self.canvas.draw_idle()
def save_csv(self):
self.plot_stats(ignore_check_auto_plot=True)
self.plot_stats(force=True)
try:
len(self.props_df)
except Exception as e:
......
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